Atheists should oppose separation of church and state?

In a nutshell: when religion is encouraged by the government, people start to resent it and it weakens. When religion is left to its own devices with no government encouragement, it flourishes, i.e. how even in 1835 Alexis de Tocqueville remarked on how much more religious America is than Europe. The idea, then, is that Christians should tear religion out of the government entirely while atheists should be in favor of a state religion.

I think that's a pretty dumb idea, but the MORE interesting part is that, when I was a Christian, I think I would have agreed with this, but now as an atheist I don't. As a Christian, I would have said that the practice of following Jesus is done best when it's done freely, without the state to coerce or "encourage" you. When the state gets into religion, it just becomes another means to control the population. (I would have said then that religion isn't always such a means.)

But the idea itself is rather dumb, because it's a false equivalency. The opposite of state religion isn't religious freedom, it's religious suppression. If you want to make a dichotomy, make it between a state that encourages a religion and a state that opposes a religion. Religious freedom is in the middle. Any encouragement of state religion, as the author of that piece says, would just encourage suppression of free thought. Religion wouldn't 'die down', it would become more militant and grow towards silencing all heretics. We've been there before.